Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA
Abstract Background Antibiotic-producing Streptomyces bacteria are ubiquitous in nature, yet most studies of its diversity have focused on free-living strains inhabiting diverse soil environments and those in symbiotic relationship with invertebrates. Results We studied the draft genomes of 73 Strep...
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doaj-309c64cc425a40c69e2e083d78962ea62021-04-11T11:21:45ZengBMCBMC Genomics1471-21642021-04-0122111110.1186/s12864-021-07546-wUnexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USACooper J. Park0Nicole A. Caimi1Debbie C. Buecher2Ernest W. Valdez3Diana E. Northup4Cheryl P. Andam5Department of Molecular, Cellular and Biomedical Sciences, University of New HampshireDepartment of Biology, University of New MexicoBuecher Biological ConsultingDepartment of Biology, University of New MexicoDepartment of Biology, University of New MexicoDepartment of Biological Sciences, University at Albany, State University of New YorkAbstract Background Antibiotic-producing Streptomyces bacteria are ubiquitous in nature, yet most studies of its diversity have focused on free-living strains inhabiting diverse soil environments and those in symbiotic relationship with invertebrates. Results We studied the draft genomes of 73 Streptomyces isolates sampled from the skin (wing and tail membranes) and fur surfaces of bats collected in Arizona and New Mexico. We uncovered large genomic variation and biosynthetic potential, even among closely related strains. The isolates, which were initially identified as three distinct species based on sequence variation in the 16S rRNA locus, could be distinguished as 41 different species based on genome-wide average nucleotide identity. Of the 32 biosynthetic gene cluster (BGC) classes detected, non-ribosomal peptide synthetases, siderophores, and terpenes were present in all genomes. On average, Streptomyces genomes carried 14 distinct classes of BGCs (range = 9–20). Results also revealed large inter- and intra-species variation in gene content (single nucleotide polymorphisms, accessory genes and singletons) and BGCs, further contributing to the overall genetic diversity present in bat-associated Streptomyces. Finally, we show that genome-wide recombination has partly contributed to the large genomic variation among strains of the same species. Conclusions Our study provides an initial genomic assessment of bat-associated Streptomyces that will be critical to prioritizing those strains with the greatest ability to produce novel antibiotics. It also highlights the need to recognize within-species variation as an important factor in genetic manipulation studies, diversity estimates and drug discovery efforts in Streptomyces.https://doi.org/10.1186/s12864-021-07546-wStreptomycesBatsGenomeAverage nucleotide identityBiosynthetic gene clusters |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Cooper J. Park Nicole A. Caimi Debbie C. Buecher Ernest W. Valdez Diana E. Northup Cheryl P. Andam |
spellingShingle |
Cooper J. Park Nicole A. Caimi Debbie C. Buecher Ernest W. Valdez Diana E. Northup Cheryl P. Andam Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA BMC Genomics Streptomyces Bats Genome Average nucleotide identity Biosynthetic gene clusters |
author_facet |
Cooper J. Park Nicole A. Caimi Debbie C. Buecher Ernest W. Valdez Diana E. Northup Cheryl P. Andam |
author_sort |
Cooper J. Park |
title |
Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA |
title_short |
Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA |
title_full |
Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA |
title_fullStr |
Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA |
title_full_unstemmed |
Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA |
title_sort |
unexpected genomic, biosynthetic and species diversity of streptomyces bacteria from bats in arizona and new mexico, usa |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2021-04-01 |
description |
Abstract Background Antibiotic-producing Streptomyces bacteria are ubiquitous in nature, yet most studies of its diversity have focused on free-living strains inhabiting diverse soil environments and those in symbiotic relationship with invertebrates. Results We studied the draft genomes of 73 Streptomyces isolates sampled from the skin (wing and tail membranes) and fur surfaces of bats collected in Arizona and New Mexico. We uncovered large genomic variation and biosynthetic potential, even among closely related strains. The isolates, which were initially identified as three distinct species based on sequence variation in the 16S rRNA locus, could be distinguished as 41 different species based on genome-wide average nucleotide identity. Of the 32 biosynthetic gene cluster (BGC) classes detected, non-ribosomal peptide synthetases, siderophores, and terpenes were present in all genomes. On average, Streptomyces genomes carried 14 distinct classes of BGCs (range = 9–20). Results also revealed large inter- and intra-species variation in gene content (single nucleotide polymorphisms, accessory genes and singletons) and BGCs, further contributing to the overall genetic diversity present in bat-associated Streptomyces. Finally, we show that genome-wide recombination has partly contributed to the large genomic variation among strains of the same species. Conclusions Our study provides an initial genomic assessment of bat-associated Streptomyces that will be critical to prioritizing those strains with the greatest ability to produce novel antibiotics. It also highlights the need to recognize within-species variation as an important factor in genetic manipulation studies, diversity estimates and drug discovery efforts in Streptomyces. |
topic |
Streptomyces Bats Genome Average nucleotide identity Biosynthetic gene clusters |
url |
https://doi.org/10.1186/s12864-021-07546-w |
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